AMBER Archive (2005)

Subject: Re: AMBER: Reference (?) for normal-mode analysis in nmode

From: David A. Case (case_at_scripps.edu)
Date: Tue May 31 2005 - 10:30:10 CDT

On Mon, May 30, 2005, Cenk Andac wrote:
>
> Could someone please refer me to a research article on
> how the nmode module of AMBER8 (with ntrun=1 option)
> computes translational, vibrational and rotational
> entropy (including equations coded in nmode) of a
> solute?

Nmode uses a rigid-rotor, harmonic osciallator (RRHO) approximation. Formulas
for thermodynamic functions can be found in almost any physical chemistry
textbook. I like Ira Levine's "Physical Chemistry", or Don McQuarrie's
"Statisical Mechanics" books, but equivalent presentations are available in
other places as well.

...dac

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